Comparative genomic and phylogenetic analyses of the mitogenome of Graptopetalum Paraguayense (N. E. Br.) Walth. 1938

TL;DR

This study reports the first complete mitochondrial genome of Graptopetalum paraguayense, revealing insights into its structure, RNA editing, and evolutionary adaptations.

Contribution

The paper provides the first complete mitogenome of G. paraguayense and identifies adaptive evolution through positive selection and interorganellar gene transfer.

Findings

The mitogenome is 242,059 bp with 50 genes and 599 RNA editing sites.

Positive selection was detected in ccmB and nad7 genes.

Evidence of chloroplast-to-mitochondrial DNA transfer was found.

Abstract

Graptopetalum paraguayense is a perennial succulent plant with ornamental, ecological, and medicinal value. Here, we present the first complete mitogenome of G. paraguayense, assembled as a circular molecule of 242,059 bp with a GC content of 43.65%. The genome contains 50 genes, including 31 protein-coding genes (PCGs), 13 tRNAs, 3 rRNAs, and 3 pseudogenes. A total of 599 RNA editing sites were identified, with a predominant effect of altering amino acid hydrophobicity (47.41% were hydrophilic-to-hydrophobic conversions). Codon usage bias analysis revealed a preference for GCU (Ala), CGA (Arg), and UUA (Leu), with the stop codon UAA exhibiting the highest RSCU value (1.94). A total of 122 repetitive sequences were identified, comprising 59 simple sequence repeats (SSRs), 1 tandem repeat, and 62 dispersed repeats. Evolutionary analysis indicated positive selection on ccmB and nad7 genes, while the majority of PCGs were under purifying selection. The mitogenome of G. paraguayense shared 57.28% sequence similarity with that of Sedum plumbizincicola. We also found evidence of chloroplast-to-mitochondrial DNA transfer, involving genes such as psaC, ndhE, ndhG, ndhI, ndhA, and ndhH. Comparative analyses identified eleven divergent hotspot regions: atp9, atp8, rpl5, cox2, ccmFn, rps7, ccmC, ccmFc, mttB, nad6, and rps13. Phylogenetic analysis confirmed the placement of G. paraguayense within the Acre clade of Crassulaceae, showing a sister relationship with S. plumbizincicola. Our study not only provides the first mitochondrial genomic resource for G. paraguayense but also reveals potential adaptive evolution through positive selection and interorganellar gene transfer, offering new perspectives on mitogenome plasticity in succulent plants.

The online version contains supplementary material available at 10.1038/s41598-025-34236-4.

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